It has long been recognised that diagnosis and treatment of disease on the basis of epidemiologic studies may not be ideal, especially when the disease is a complex one having multiple causative factors and many subtypes with possibly wildly varying outcomes for the patient. This has recently led to an increased emphasis on so-called “personalised medicine”, whereby specific characteristics of the individual are taken info account when providing care.
An important development in the move towards personalised care has been the ability to identify molecular markers which are associated with a particular disease state or which are predictive of the individual's response to a particular treatment.
For example, in relation to breast cancer, the estrogen receptor (ER) or HER2/neu (ErbB-2) status of a tumour can be used in determining a patient's suitability for therapies that target these molecules in the tumor cells. These molecular markers are examples of “companion diagnostics” which are used in conjunction with traditional tests such as histological status in order to guide treatment regimes.
In cancer cases where a tumour has metastasized, it is important to determine the tissue of origin of the tumour. The current diagnostic standard in such cases includes imaging, serum tests and immunohistochemistry (IHC) using one or more of a panel of known antibodies of different tumour specificity (Pavlidis et al, Eur J Cancer 39, p 1990 (2003); Burton et al, JAVA 280, p 1245 (1998); Varadhachary et al, Cancer 100, p 1776 (2004)). For approximately 3-5% of all cases, known as Cancer of Unknown Primary (CUP), these conventional approaches do not reach a definitive diagnosis, although some may eventually be solved with further, more extensive investigations (Horlings et al, J Clin Oncol 26, p 4435 (2008); Raab et al, Cancer 104, p 2205 (2005)). The range of tests able to be performed can depend not only on an individual patient's ability to tolerate potentially invasive, costly and time consuming diagnostic procedures, but also on the diagnostic tools at the clinician's disposal, which may vary between hospitals and countries.
To date, most diagnostic protocols are primarily reliant on microscopy, single gene or protein biomarkers (IHC) and imaging techniques such as MRI and PET Scan. Unfortunately, these techniques all have limitations and may not on their own provide adequate information to diagnose widely metastasized tumours, poorly differentiated malignancies, rare subtypes or unusual presentations of common cancers.
It has been hypothesized that the information gained from gene expression profiling can be used as a companion diagnostic to the above protocols, helping to confirm or refine the predicted primary origin in a focused and efficient manner.
Since the advent of various robotic and high throughput genomic technologies, including RT-PCR and microarray, several groups (van Laar et al, Int J Cancer 125, p 1390 (2009); Rosenfeld et al, Nature Biotechnology 26, p 462 (2008); Tothill et al, Cancer Res 65, p 4031 (2005); Bloom at al, Am J Pathol 164, p 9 (2004); Monzon et al, J Clin Oncol 27, p 2503 (2009); Ramaswamy et al, PNAS 98, 15149 (2001)) have investigated the use of gene expression data to predict the primary origin of a metastatic tumor. Prediction accuracies in the literature, range from 78% to 89%.
A number of gene expression based, commercial diagnostic services have arisen since the sequencing of the human genome, offering a range of personalized diagnostic and prognostic assays. These services represent a significant advance in patient access to personalized medicine. However the requirement of shipping fresh or preserved human tissue to an interstate or international reference laboratory has the potential to expose sensitive biological molecules to adverse weather conditions and logistical delays, in some parts of the world it may also be prohibitively expensive to ship human tissue to a reference laboratory in a timely fashion, thus limiting access to this new technology.
Most current commercially available gene-expression based cancer tests use a proprietary “diagnostic” microarray or PCR-based assay (van Laar et al; Rosenfeld et al; Dumur et al, J Mol Diagn 10, p 67 (2008)). Such arrays allow assaying of a small set of genes chosen for a particular purpose and are custom manufactured for that purpose. Because of the limited set of genes that are quantified by these existing assays, the data generated generally cannot be used for multiple diagnostic or prognostic analyses if a different set of genes is required. Furthermore, whatever data is generated, it is generally not accessible to the clinician requesting the test should it be desired to conduct further investigations or compile a custom database of gene expression data for research purposes.
In view of the above deficiencies, it is desirable to provide a more flexible and efficient method and system for diagnosis and prognosis of a patient based on expression of multiple biological markers.